Superflat world customization visually replaces water ID with Air ID
Upon creating a super-flat world selecting or adding/editing in 'minecrat:water' it is changed to 'minecraft:air' this is only a visual glitch and does not effect the world's generation.
Gif explaining the Visual glitch a bit more: http://zippy.gfycat.com/BreakableFlashyArieltoucan.gif